On-Slide Staining by Primer Extension

ABSTRACT

A method for analyzing planar sample is provided. In some cases the method comprises: (a) incubating the planar sample with a capture agent that is linked to an oligonucleotide, wherein the capture agent specifically binds to complementary sites in the planar sample; (b) reading a fluorescent signal caused by extension of a primer that is hybridized to the oligonucleotide, using fluorescence microscopy. Several implementations of the method, and multiplexed versions of the same, are also provided.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH

This invention was made with Government support under contractW81XWH-12-1-0591 awarded by the Department of Defense and undercontracts GM104148 and HHSN268201000034C awarded by the NationalInstitutes of Health. The Government has certain rights in theinvention.

BACKGROUND

Several major approaches have been used so far for single-cell antigencytometry. Among the most popular are single cell PCR, fluorescenceactivated flow cytometry, mass cytometry and single cell sequencing.These (fluorescence and mass-based cytometry) approaches are limitedfrom either inability to breach the multiplexing levels of more than 100parameters per analyte (cell in this case) or from inability to achievehigh throughput (single cell sequencing). Also these methods are notappropriate or readily modified to enable cell multiplexed analysis ofarchived tissues and slide based samples.

Disclosed herein are several related methods for capture agent detectionthat are based on labeling the capture agent with DNA and subsequentdetection of this DNA by primer extension.

SUMMARY

Provided herein is a method for analyzing a planar sample. In certainembodiments, the method comprises: (a) incubating the planar sample(e.g., a tissue section such as a formalin-fixed, paraffin-embedded(FFPE) section) with a capture agent under conditions by which thecapture agent specifically binds to complementary sites in the planarsample, wherein: (i) the capture agent is linked to a double-strandedoligonucleotide that comprises a first strand and a second strand; (ii)the capture agent is linked to a double-stranded oligonucleotide by the5′ end of the first strand; and (iii) the 3′ end of the first strand isrecessed relative to the 5′ end of the second strand, thereby producingan 5′-overhang; (b) crosslinking the capture agent to planar sample; (c)contacting the planar sample with a polymerase and a nucleotide mix,thereby adding one or more nucleotides to the overhang; and (d) readinga fluorescent signal generated by addition of the one or morenucleotides to the overhang using fluorescence microscopy, therebyproducing an image showing the pattern of binding of the capture agentto the planar sample.

In certain embodiments, the method includes contacting the planar samplewith a polymerase and a nucleotide mix that comprises a fluorescentnucleotide, thereby adding the fluorescent nucleotide to the overhang;and reading a fluorescent signal generated by addition of thefluorescent nucleotide to the overhang. In these embodiments, thefluorescent signal that is read may be, for example, emitted directlyfrom the added nucleotide or may be a FRET signal generated by energytransfer, e.g., between two fluorescent nucleotides that are added tothe overhang or between a first fluorescent nucleotide added to overhangand a second fluorescent nucleotide that is present in the secondstrand.

In alternative embodiments, extension of the first strand may remove aquencher from a quenched fluorescently labeled oligonucleotide that ishybridized to the second strand, downstream from the first strand.

Also provided herein is an capture agent that is linked to adouble-stranded oligonucleotide, wherein: (i) the double-strandedoligonucleotide comprises a first strand and a second strand; (ii) thecapture agent is linked to the 5′ end of the first strand; and (iii) the3′ end of the first strand is recessed relative to the 5′ end of thesecond strand, thereby producing an 5′-overhang.

Also provided herein is an capture agent composition comprising aplurality of capture agents that recognize different complementarysites. In these embodiments, each of the capture agents is linked to adouble-stranded oligonucleotide that comprises a first strand and asecond strand; the capture agents are linked to a double-strandedoligonucleotide by the 5′ end of first strand; the 3′ end of the firststrand in each of the double-stranded oligonucleotides is recessedrelative to the 5′ end of the second strand, thereby producing an5′-overhang; and the overhang is different for each of the captureagents. In some cases, the sequence of the first strand is the same foreach of the capture agents; and the sequence of the second strand isdifferent for each of the capture agents.

While DNA sequences are routinely set forth in 5′ to 3′ direction, forthe ease description, certain DNA sequences in the text below aredescribed in the 3′ to 5′ direction. In each such case thedirectionality is specifically annotated.

In embodiments that use a reversible terminator (“reversible terminator”approach), the overhangs may be of the formula 3′-N_(4n)N₁/N₂/N₃-5′optionally followed by short stretch (e.g., 1-5 residues) of randomnucleotides on the 5′ end to increase the overall polymerase residenceon the DNA duplex, where N₁, N₂, N₃ and N₄ are different nucleotidesselected from G, A, T and C and n is 0, 1 or more (i.e., populationcontains single nucleotide overhangs of nucleotides N₁, N₂ and N₃ or thepopulation of overhangs comprises two nucleotide overhangs of sequence3′-N₄N₁-5′, 3′-N₄N₂-5′ and 3′-N₄N₃-5′-5′ and, optionally overhangs ofsequence, 3′-N₄N₄N₁-5′, 3′-N₄N₄N₂-5′ and 3′-N₄N₄N₃-5′ and so on (e.g.,four nucleotide overhangs of sequence 3′-N₄N₄N₄N₁-5′, 3′-N₄N₄N₄N₂-5′ and3′-N₄N₄N₄N₃-5′).

In these embodiments, the overhangs may be of a more general formula3′-XN₁/N₂/N₃-5′, where N₁, N₂, N₃ are different nucleotides selectedfrom G, A, T and C and X is a nucleotide stretch of bases Xi (such thatXi are different nucleotides selected from G, A, T and C) of randomcomposition and length (i.e., the population of overhangs comprises twonucleotide overhangs of sequence 3′-X₁N₁-5′, 3′-X₁N₂-5′ and 3′-X₁N₃-5′and, optionally overhangs of sequence, 3′-N₁X₁X₂-5′, 3′-N₂X₁X₂-5′ and3′-N₃X₁X₂-5′ and so on (e.g., four nucleotide overhangs of sequence3′-N₁X₁X₂X₃-5′, 3′-N₂X₁X₂X₃-5′ and 3′-N₃X₁X₂X₃-5′). In many embodiments,this population additionally contains single nucleotide overhangs ofnucleotides N₁, N₂ and N₃.

In embodiments that rely on a “missing base” approach, the overhangs maybe of the formula 3′-YN₁/N₂-5′, optionally followed by short stretch(e.g., 1-5 residues) of random nucleotides on the 5′ end to increase theoverall polymerase residence on the DNA duplex, wherein Y is anucleotide sequence of length n (n is 0, 1 or more) composed of bases N₃and N₄, wherein nucleotide N₃ is in odd positions and nucleotide N₄ isin even positions, counting from the start of the overhang and N₁, N₂,N₃ and N₄ are different nucleotides selected from G, A, T and C. Forexample, the population of overhangs comprises 5′ overhangs of sequence3′-N₁-5′ and 3′-N₂-5′ or optionally 3′-N₃N₁-5′ and 3′-N₃N₂-5′ or3′-N₃N₄N₁-5′ and 3′-N₃N₄N₂-5′ and, optionally, overhangs of sequence3′-N₃N₄N₃N₁-5′ and 3′-N₃N₄N₃N₂-5′ and so on (e.g., overhangs of sequence3′-N₃N₄N₃N₄N₁-5′ and 3′-N₃N₄N₃N₄N₂-5′ and then 3′-N₃N₄N₃N₄N₃N₁-5′ and3′-N₃N₄N₃N₄N₃N₂-5′).

In these embodiments the overhangs may also be of a more general formula3′-YN₁/N₂-5′, wherein Y is a nucleotide sequence of length n (n is 0, 1or more) composed of alternating random length stretches of bases N₃ andN₄ such that the order number of N₃—stretches is odd and of N₄ stretchesis even and wherein N₁, N₂, N₃ and N₄ are different nucleotides selectedfrom G, A, T and C. For example, the population of overhangs comprisesoverhangs of sequence 3′-N₁-5′ and 3′-N₂-5′ or optionally 3′-N₃N₃N₁-5′and 3′-N₃N₃N₂-5′ or 3′-N₃N₃N₄N₁-5′ and 3′-N₃N₃N₄N₂-5′ and, optionally,overhangs of sequence 3′-N₃N₃N₃N₃N₄N₄N₃N₃N₃N₁-5′ and3′-N₃N₃N₃N₃N₄N₄N₃N₃N₃N-5′ 2 and so on).

Also provided is a method for analyzing a planar sample in a multiplexway. In certain embodiments, this method comprises: (a) incubating theplanar sample with the above-summarized capture agent composition underconditions by which the capture agents specifically bind tocomplementary sites in the planar sample; (b) crosslinking the captureagent to planar sample; (c) contacting the planar sample with apolymerase and either an incomplete nucleotide mix of labeled andunlabeled bases or a nucleotide mix where some or all bases arefluorescent and some or all bases constitute reversible terminatornucleotides or fluorescent reversible terminator nucleotides; and (d)reading, using fluorescence microscopy, a fluorescent signal generatedby addition of a fluorescent nucleotide to some but not all of thecapture agents.

In certain embodiments, the method comprises: (c) contacting the planarsample with a polymerase and: (i) a nucleotide mix that comprisesfluorescent nucleotides that are complementary to N₁, N₂ and N₃ and areversible terminator nucleotide that is complementary to N₄ or (ii) anucleotide mix that comprises fluorescent reversible terminatornucleotides that are complementary to N₁, N₂ and N₃ and a reversibleterminator nucleotide that is complementary to N₄ or (iii) a nucleotidemix that comprises fluorescent nucleotides that are complementary to N₁,and N₂, an unlabeled nucleotide that is complementary to N₃, and nonucleotide that is complementary to N₄, thereby adding fluorescentnucleotides onto the double-stranded oligonucleotides of some but notall of the capture agents; and (d) reading, using fluorescencemicroscopy a fluorescent signal generated by addition of a fluorescentnucleotide to some but not all of the capture agents.

In certain embodiments, the overhangs may be of the formula3′-N_(4n)N₁/N₂/N₃-5′ optionally followed by short stretch (e.g., 1-5residues) of random nucleotides on the 5′ end to increase the overallpolymerase residence on the DNA duplex, or 3′-XN₁/N₂/N₃-5′, where N₁,N₂, N₃ are different nucleotides selected from G, A, T and C and n is 1or more and X is a nucleotide stretch of bases Xi (such that Xi aredifferent nucleotides selected from G, A, T and C) of random compositionand length; and step (c) comprises contacting the planar sample with apolymerase and a nucleotide mix that comprises fluorescent nucleotides(being reversible terminators or not) that are complementary to N₁, N₂and N₃ and an unlabeled reversible terminator nucleotide that iscomplementary to N₄. These embodiments may further comprise (e)inactivating the fluorescent signal, simultaneously deprotecting thereversible terminator nucleotide (f) blocking the planar sample; and (g)repeating steps (c), (d), (e) and (f). In some embodiments, step (g) maycomprise repeating steps (c), (d), (e) and (f) multiple times.

Alternatively, in some embodiments, the overhangs may be of the formula3′-YN₁/N₂-5′, optionally followed by short stretch (e.g., 1-5 residues)of random nucleotides on the 5′ end to increase the overall polymeraseresidence on the DNA duplex, wherein Y is a nucleotide sequence oflength n (n is 0, 1 or more) composed of bases N₃ and N₄, whereinnucleotide N₃ is in odd positions and nucleotide N₄ is in evenpositions, counting from the start of the overhang and N₁, N₂, N₃ and N₄are different nucleotides selected from G, A, T and C, and step (c)comprises contacting the planar sample with a polymerase and anucleotide mix that comprises fluorescent nucleotides that arecomplementary to N₁, and N₂, an unlabeled nucleotide that iscomplementary to N₃ and no nucleotide that is complementary to N₄. Theseembodiments may further comprise (e) inactivating the fluorescentsignal, (f) blocking the planar sample and (g) contacting the planarsample with a polymerase and an unlabeled nucleotide that iscomplementary to N₄; and (h) repeating steps (c), (d), (e) and (f). Insome cases, step (g) may comprise repeating steps (c), (d), (e) and (f)multiple times.

In alternative embodiments, the double-stranded oligonucleotides mayeach comprise a fluorescently labeled oligonucleotide hybridized to thesecond strand downstream from first strand, wherein the fluorescentlylabeled oligonucleotide comprises a quencher and extension of the firststrand removes the quencher from some but not all of the quenchedfluorescently labeled oligonucleotides, thereby generating a fluorescentsignal for some but not all of the capture agents.

In other embodiments, the capture agent is linked to a single strandedoligonucleotide, which can be either unlabeled or labeled with FRETacceptor fluorophore. Such a single stranded nucleotide incorporates adedicated sequence that hybridizes to a complementary oligonucleotidewhich is to be extended with unlabeled base or with a base labeled witha FRET excitation fluorophore, thereby generating a fluorescent signalfor some but not all of the capture agents.

BRIEF DESCRIPTION OF THE FIGURES

The patent or application file contains at least one drawing executed incolor. Copies of this patent or patent application publication withcolor drawing(s) will be provided by the Office upon request and paymentof the necessary fee.

The skilled artisan will understand that the drawings, described below,are for illustration purposes only. The drawings are not intended tolimit the scope of the present teachings in any way.

FIG. 1A-1B (A) schematically illustrates a detection reagent composed ofa combination of a capture agent that is conjugated to a double-strandedoligonucleotide. Upon detection and removal of unbound detection reagentthe binding pattern is rendered by polymerase driven primer extension.Panel (B) schematically illustrates three approaches for linking thecapture agent (an antibody in this case, but not exclusing otherpossible capture agents) to a double stranded oligonucleotide (i.e., bychemical conjugation of the upper strand oligonucleotide to the captureagent; using streptavidin as an intermediate to connect biotinylatedantibody and biotinylated oligonucleotide; and by linking biotinlatedoligonucleotide to antibody chemically conjugated to streptavidin).

FIG. 2 schematically illustrates examples of capture agents that arebound to double-stranded oligonucleotides that have different overhangs.Such different overhangs represent a strategy to increase signalharvested from a particular capture agent by multiplication of positionsin lower strand oligonucleotide complementary to detector base (dU inthis case). The lower panel also shows how a different base labeled witha different fluorophore can be used as a FRET excitation pair for the“Detector” base. SEQ ID NOS: 1-4.

FIG. 3 schematically illustrates several cycles of a multiplexeddetection method that relies on reversible dye terminators.

FIG. 4 schematically illustrates several cycles of a multiplexeddetection method that relies on leaving out one of the four nucleotidesper cycle.

FIG. 5A-5D schematically illustrates an exemplary design ofoligonucleotide duplexes for “reversible terminator” and “missing base”multiplexing methods. SEQ ID NOS: 5-12.

FIG. 6 schematically illustrates an exemplary design of oligonucleotideduplexes for a strategy that allows one to reduce the length of thelower strand oligonucleotide, creating an overhang in the case of highlymultiplexed capture agent panels. SEQ ID NOS: 13-30.

FIG. 7 schematically illustrates an example of a detection method thatrelies on removing a quencher from a labeled oligonucleotide by nicktranslation. SEQ ID NOS: 31-35.

FIG. 8 schematically illustrates a multiplexed detection method thatrelies on removing quenchers from labeled oligonucleotides. Step 1: SEQID NOS 36-44, Step 2: SEQ ID NOS: 45-52, Step 3: SEQ ID NOS: 53-60, Step4: SEQ ID NOS: 61-67.

FIGS. 9A and 9B schematically illustrate an embodiment that relies oncyclical re-annealing of polymerase priming nucleotides and a variant ofthe same approach that utilizes FRET. SEQ ID NOS: 68-80.

FIG. 10 schematically illustrate an embodiment that relies on cyclicalre-annealing of polymerase priming nucleotides and a variant of the sameapproach that utilizes FRET. SEQ ID NOS: 81-86.

FIGS. 11A-11C shows an anti-CD4 antibody linked to oligonucleotideduplex designed for rendering staining by primer extension (panel A) anddata obtained from labeled population of spleen cells in suspension inthe absence of polymerase (panel B) and in the presence of polymerase(panel C). SEQ ID NOS: 87 and 88.

FIGS. 12A-12D shows data obtained from labeling by primer extension apopulation of spleen cells preattached on the slide. Cells wereco-stained with “regular” TCRb-FITC antibody and CD4 antibody linked tooligonucleotide duplex designed for rendering staining by primerextension.

FIGS. 13A-13D show schematic illustration of two capture agents CD4 andCD8 linked to oligonucleotide duplexes (panel A) and data obtained froma multiplexed method whereby staining by this capture agents wassequentially detected on spleen cells smeared on a slide using a“reversible terminator” method (panels C-D). SEQ ID NOS: 89-92.

FIG. 14 shows a schematic diagram of an experiment testing multiplexedstaining by “missing base” approach. Mouse spleen samples were barcodedby pan-leukocytic CD45 antibody conjugated to per sample specificoligonucleotide duplexes. Samples were mixed after staining and mixturewas resolved by sequential rendering of CD45-oligonucleotide variants.

FIG. 15 is 12 panels of images showing the first 6 cycles of renderingthe 30 populations barcoded by CD45 (as per scheme on FIG. 14 ). Twopopulations were co-detected per cycle of rendering. In each cyclecontrol image was acquired after fluorescence inactivation.

DEFINITIONS

Unless defined otherwise herein, all technical and scientific terms usedherein have the same meaning as commonly understood by one of ordinaryskill in the art to which this invention belongs. Although any methodsand materials similar or equivalent to those described herein can beused in the practice or testing of the present invention, the preferredmethods and materials are described.

All patents and publications, including all sequences disclosed withinsuch patents and publications, referred to herein are expresslyincorporated by reference.

Numeric ranges are inclusive of the numbers defining the range. Unlessotherwise indicated, nucleic acids are written left to right in 5′ to 3′orientation; amino acid sequences are written left to right in amino tocarboxy orientation, respectively.

The headings provided herein are not limitations of the various aspectsor embodiments of the invention. Accordingly, the terms definedimmediately below are more fully defined by reference to thespecification as a whole.

Unless defined otherwise, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this invention belongs. Singleton, et al., DICTIONARYOF MICROBIOLOGY AND MOLECULAR BIOLOGY, 2D ED., John Wiley and Sons, NewYork (1994), and Hale & Markham, THE HARPER COLLINS DICTIONARY OFBIOLOGY, Harper Perennial, N.Y. (1991) provide one of skill with thegeneral meaning of many of the terms used herein. Still, certain termsare defined below for the sake of clarity and ease of reference.

As used herein, the term “biological feature of interest” refers to anypart of a cell that can be indicated by binding to a capture agent.Exemplary biological features of interest include cell walls, nuclei,cytoplasm, membrane, keratin, muscle fibers, collagen, bone, proteins,nucleic acid (e.g., mRNA or genomic DNA, etc). fat, etc. A biologicalfeature of interest can also be indicated by immunohistological methods,e.g., a capture agent that is linked to an oligonucleotide. In theseembodiments, the capture agent binds to an site, e.g., a proteinepitope, in the sample. Exemplary epitopes include, but are not limitedto carcinoembryonic antigen (for identification of adenocarcinomas,cytokeratins (for identification of carcinomas but may also be expressedin some sarcomas) CD15 and CD30 (for Hodgkin's disease), alphafetoprotein (for yolk sac tumors and hepatocellular carcinoma), CD117(for gastrointestinal stromal tumors), CD10 (for renal cell carcinomaand acute lymphoblastic leukemia), prostate specific antigen (forprostate cancer), estrogens and progesterone (for tumouridentification), CD20 (for identification of B-cell lymphomas), CD3 (foridentification of T-cell lymphomas). Complementary nucleic acidmolecules (e.g., DNA and/or RNA) in the sample provide bindingcomplementary sites for oligonucleotide probes.

As used herein, the term “multiplexing” refers to using more than onelabel for the simultaneous or sequential detection and measurement ofbiologically active material.

As used herein, the terms “antibody” and “immunoglobulin” are usedinterchangeably herein and are well understood by those in the field.Those terms refer to a protein consisting of one or more polypeptidesthat specifically binds an antigen. One form of antibody constitutes thebasic structural unit of an antibody. This form is a tetramer andconsists of two identical pairs of antibody chains, each pair having onelight and one heavy chain. In each pair, the light and heavy chainvariable regions are together responsible for binding to an antigen, andthe constant regions are responsible for the antibody effectorfunctions.

The recognized immunoglobulin polypeptides include the kappa and lambdalight chains and the alpha, gamma (IgG₁, IgG₂, IgG₃, IgG₄), delta,epsilon and mu heavy chains or equivalents in other species. Full-lengthimmunoglobulin “light chains” (of about 25 kDa or about 214 amino acids)comprise a variable region of about 110 amino acids at the NH₂-terminusand a kappa or lambda constant region at the COOH-terminus. Full-lengthimmunoglobulin “heavy chains” (of about 50 kDa or about 446 aminoacids), similarly comprise a variable region (of about 116 amino acids)and one of the aforementioned heavy chain constant regions, e.g., gamma(of about 330 amino acids).

The terms “antibodies” and “immunoglobulin” include antibodies orimmunoglobulins of any isotype, fragments of antibodies which retainspecific binding to antigen, including, but not limited to, Fab, Fv,scFv, and Fd fragments, chimeric antibodies, humanized antibodies,minibodies, single-chain antibodies, and fusion proteins comprising anantigen-binding portion of an antibody and a non-antibody protein. Alsoencompassed by the term are Fab′, Fv, F(ab′)2, and or other antibodyfragments that retain specific binding to antigen, and monoclonalantibodies. Antibodies may exist in a variety of other forms including,for example, Fv, Fab, and (Fab′)₂, as well as bi-functional (i.e.bi-specific) hybrid antibodies (e.g., Lanzavecchia et al., Eur. J.Immunol. 17, 105 (1987)) and in single chains (e. g., Huston et al.,Proc. Natl. Acad. Sci. U.S.A., 85, 5879-5883 (1988) and Bird et al.,Science, 242, 423-426 (1988), which are incorporated herein byreference). (See, generally, Hood et al., “Immunology”, Benjamin, N.Y.,2nd ed. (1984), and Hunkapiller and Hood, Nature, 323, 15-16 (1986).

The term “specific binding” refers to the ability of a binding reagentto preferentially bind to a particular analyte that is present in ahomogeneous mixture of different analytes. In certain embodiments, aspecific binding interaction will discriminate between desirable andundesirable analytes in a sample, in some embodiments more than about 10to 100-fold or more (e.g., more than about 1000- or 10,000-fold).

In certain embodiments, the affinity between a binding reagent andanalyte when they are specifically bound in a capture agent/analytecomplex is characterized by a K_(D) (dissociation constant) of less than10⁻⁶M, less than 10⁻⁷ M, less than 10⁻⁸ M, less than 10⁻⁹ M, less than10⁻⁹ M, less than 10⁻¹¹ M, or less than about 10⁻¹² M or less.

A “plurality” contains at least 2 members. In certain cases, a pluralitymay have at least 2, at least 5, at least 10, at least 100, at least1000, at least 10,000, at least 100,000, at least 10⁶, at least 10⁷, atleast 10⁸ or at least 10⁹ or more members.

As used herein, the term “labeling” refers to attaching a detectablefluorophore to specific sites in a sample (e.g., sites containing anepitope for the antibody being used, for example) such that the presenceand/or abundance of the sites can be determined by evaluating thepresence and/or abundance of the label.

As used herein, the term “planar sample” refers to a substantiallyplanar, i.e., two dimensional, material that contains cells. A planarcellular sample can be made by, e.g., growing cells on a planar surface,depositing cells on a planar surface, e.g., by centrifugation, or bycutting a three dimensional object that contains cells into sections andmounting the sections onto a planar surface, i.e., producing a tissuesection. The cells may be fixed using any number of reagents includingformalin, methanol, paraformaldehyde, methanol:acetic acid etc.

As used herein, the term “tissue section” refers to a piece of tissuethat has been obtained from a subject, fixed, sectioned, and mounted ona planar surface, e.g., a microscope slide.

As used herein, the term “formalin-fixed paraffin embedded (FFPE) tissuesection” refers to a piece of tissue, e.g., a biopsy that has beenobtained from a subject, fixed in formaldehyde (e.g., 3%-5% formaldehydein phosphate buffered saline) or Bouin solution, embedded in wax, cutinto thin sections, and then mounted on a microscope slide.

As used herein, the term “spatially-addressable measurements” refers toa set of values that are each associated with a specific position on asurface. Spatially-addressable measurements can be mapped to a positionin a sample and can be used to reconstruct an image of the sample.

A “diagnostic marker” is a specific biochemical in the body which has aparticular molecular feature that makes it useful for detecting adisease, measuring the progress of disease or the effects of treatment,or for measuring a process of interest.

A “pathoindicative” cell is a cell which, when present in a tissue,indicates that the animal in which the tissue is located (or from whichthe tissue was obtained) is afflicted with a disease or disorder. By wayof example, the presence of one or more breast cells in a lung tissue ofan animal is an indication that the animal is afflicted with metastaticbreast cancer.

The term “complementary site” is used to refer to an epitope for anantibody or aptamer, or a nucleic acid molecule if the capture agent isan oligonucleotide probe. Specifically, if the capture agent is anantibody, then the complementary site for the capture agent is theepitope in the sample to which the antibody binds. If the capture agentis an oligonucleotide probe, then the complementary site for the captureagent is a complementary sequence in a DNA or RNA molecule in thesample.

The term “epitope” as used herein is defined as small chemical groups onthe antigen molecule that is bound to by an antibody. An antigen canhave one or more epitopes. In many cases, an epitope is roughly fiveamino acids or sugars in size. One skilled in the art understands thatgenerally the overall three-dimensional structure or the specific linearsequence of the molecule can be the main criterion of antigenicspecificity.

A “subject” of diagnosis or treatment is a plant or animal, including ahuman. Non-human animals subject to diagnosis or treatment include, forexample, livestock and pets.

As used herein, the term “incubating” refers to maintaining a planarsample and capture agent under conditions (which conditions include aperiod of time, a temperature, an appropriate binding buffer and a wash)that are suitable for specific binding of the capture agent to molecules(e.g., epitopes or complementary nucleic acid) in the planar sample.

As used herein, the term “capture agent” refers to an agent that canspecifically bind to complementary sites in a planar sample. Exemplarycapture agents include, e.g., an antibody, an aptamer, and anoligonucleotide probe (which may be DNA or RNA) that hybridizes to abinding site.

As used herein, the term “capture agent that is linked to a doublestranded oligonucleotide” refers to a capture agent, e.g., an antibodyor an oligonucleotide probe, that is non-covalently (e.g., via astreptavidin/biotin interaction) or covalently (e.g., via a clickreaction or the like) linked to an oligonucleotide (which may becomposed of two single-stranded oligonucleotide strands that arehybridized together) in a way that the capture agent can still bind toits binding site and the 3′ end of one of the oligonucleotides isaccessible to a polymerase. The oligonucleotide and the capture agentmay be linked via a number of different methods, including those thatuse maleimide or halogen-containing group, which are cysteine-reactive.

As used herein, the term “oligonucleotide” refers to a multimer of atleast 10, e.g., at least 15 or at least 30 nucleotides. In someembodiments, an oligonucleotide may be in the range of 15-200nucleotides in length.

As used herein, the term “reading” in the context of reading afluorescent signal, refers to obtaining an image by scanning or bymicroscopy, where the image shows the pattern of fluorescence as well asthe intensity of fluorescence in a field of view.

As used herein, the term “primer” is an oligonucleotide, either naturalor synthetic, that is capable, upon forming a duplex with apolynucleotide template, of acting as a point of initiation of nucleicacid synthesis and being extended from its 3′ end along the template sothat an extended duplex is formed. The sequence of nucleotides addedduring the extension process is determined by the sequence of thetemplate polynucleotide. Usually primers are extended by a DNApolymerase. A primer may be at least 10, e.g., at least 15 or at least30 nucleotides in length.

As used herein, the term “single nucleotide 5′ overhang” refers to a 5′overhang, where the overhang is a single nucleotide in length. Likewise,a “two nucleotide 5′ overhang” is a 5′ overhang, where the overhang istwo nucleotides in length. The 3′ end is recessed in a 5′ overhang.

In certain cases, the various nucleotides of an overhang may be referredto by their position, e.g., “first position” and “second position”. Inthese cases, the “position” is relative to the recessed 3′ end. As such,in a multiple base 5′ overhang, the “first” position of the overhang isimmediately adjacent to the recessed 3′ end and the “second” position ofthe overhang is immediately adjacent to the first position.

In certain cases, the complementary strands of a double strandedoligonucleotide may be referred to herein as being the “first” and“second” or the “top” and “bottom” strands. The assignment of a strandas being a “top” or “bottom” strand is arbitrary and does not imply anyparticular orientation, function or structure.

As used herein, the term “signal generated by”, in the context ofreading a fluorescent signal generated by addition of the fluorescentnucleotide, refers to a signal that is emitted directly from thefluorescent nucleotide, a signal that is emitted indirectly via energytransfer to another fluorescent nucleotide (i.e., by FRET).

As used herein, the term “fluorescently labeled oligonucleotidecomprising a quencher” refers to an oligonucleotide that contains afluorophore and a quencher, wherein the quencher quenches thefluorophore in the same oligonucleotide.

As used herein, the term “different” in the context of different 5′overhangs that are different, refers to overhangs that have a differentsequence. Overhangs of different lengths (e.g., GATC vs GAT) implicitlyhave a different sequence, even through one sequence may be encompassedby the other.

As used herein, the term “adding to an overhang”, in the context ofadding one or more nucleotides to an overhang, refers to addingnucleotides to the recessed 3′ end of a 5′ overhang using the overhangas a template.

As used herein, the term “overhangs of the formula 3′-N_(4n)N₁/N₂/N₃-5′followed by an optional short stretch (e.g., 1-5 residues) of randomnucleotides on the 5′ end to increase the overall polymerase residenceon the DNA duplex, where N₁, N₂, N₃ and N₄ are different nucleotidesselected from G, A, T and C and n is 0, 1 or more”, refers to apopulation of overhangs that contains single nucleotide overhangs ofnucleotides N₁, N₂ and N₃ or the population of overhangs comprises twonucleotide overhangs of sequence 3′-N₄N₁-5′, 3′-N₄N₂-5′ and3′-N₄N₃-5′-5′ and, optionally overhangs of sequence, 3′-N₄N₄N₁-5′,3′-N₄N₄N₂-5′ and 3′-N₄N₄N₃-5′ and so on (e.g., four nucleotide overhangsof sequence 3′-N₄N₄N₄N₁-5′, 3′-N₄N₄N₄N₂-5′ and 3′-N₄N₄N₄N₃-5′).

As used herein, the term “overhangs of the formula 3′-YN₁/N₂-5′,optionally followed by short stretch (e.g., 1-5 residues) of randomnucleotides on the 5′ end to increase the overall polymerase residenceon the DNA duplex, wherein Y is a nucleotide sequence of length n (n is0, 1 or more) composed of bases N₃ and N₄, wherein nucleotide N₃ is inodd positions and nucleotide N₄ is in even positions, counting from thestart of the overhang and N₁, N₂, N₃ and N₄ are different nucleotidesselected from G, A, T and C” refers to a population of overhangs ofsequence 3′-N₁-5′ and 3′-N₂-5′ or optionally 3′-N₃N₁-5′ and 3′-N₃N₂-5′or 3′-N₃N₄N₁-5′ and 3′-N₃N₄N₂-5′ and, optionally, overhangs of sequence3′-N₃N₄N₃N₁-5′ and 3′-N₃N₄N₃N₂-5′ and so on (e.g., overhangs of sequence3′-N₃N₄N₃N₄N₁-5′ and 3′-N₃N₄N₃N₄N₂-5′ and then 3′-N₃N₄N₃N₄N₃N₁-5′ and3′-N₃N₄N₃N₄N₃N₂-5′).

As used herein, the term “alternating stretches” refers to twonucleotides stretches, where one “stretch” is a contiguous sequence of,e.g., up to 10, of the same nucleotide (e.g., a G, A, T or C), and thesecond stretch is contiguous sequence of, e.g., up to 10, of a differentnucleotide, that alternate with one another, i.e., one stretch (e.g., astring of T's) occupies the odd positions and the other stretch (e.g., astring of A's) occupies the even positions.

As used herein, the term “incomplete nucleotide mix” comprises anucleotide mix that contains one, two or three nucleotides (but not allfour nucleotides) selected from G, A, T and C. The nucleotides may belabeled or unlabeled.

As used herein, the term “reversible terminator” refers to a chemicallymodified nucleotide base that when incorporated into growing DNA strandby DNA polymerase blocks further incorporation of bases. Such“reversible terminator” base and DNA strand can be deprotected bychemical treatment and following such deprotection DNA strand can befurther extended by DNA polymerase.

As used herein, the term “fluorescently labeled reversible terminator”refers to a “reversible terminator” base which is labeled by fluorophorethrough linker cleavable by same treatment which is used to deprotectthe DNA strand which ends with this base. Deprotecting the“fluorescently labeled reversible terminator” simultaneously activatesthe DNA strand for further extension and removes the fluorescent labelfrom it.

For ease of description, many of the sequences described herein arewritten out in the 3′ to 5′ direction.

Other definitions of terms may appear throughout the specification.

DETAILED DESCRIPTION

In some embodiments the method comprises labeling a planar sample (e.g.,an FFPE section mounted on a planar surface such as a microscope slide)with a capture agent that specifically binds to complementary sites inthe planar sample. This step is done under conditions by which thecapture agent binds to complementary sites in the planar sample, methodsfor which are well known. In these embodiments, the capture agent islinked to a double-stranded oligonucleotide that comprises a firststrand and a second strand (e.g., two oligonucleotide that arehybridized together) and the capture agent is linked (covalently ornon-covalently via a biotin) to the double-stranded oligonucleotide bythe 5′ end of the first strand, and the 3′ end of the first strand isrecessed relative to the 5′ end of the second strand, thereby definingan overhang. After the capture agent has bound to the planar sample, thecapture agent is cross-linked the planar sample. This crosslinking stepmay be done using any amine-to-amine crosslinker (e.g. formaldehyde,disuccinimiyllutarate or another reagents of similar action) although avariety of other chemistries can be used to cross-link the capture agentto the planar sample if desired. The method comprises reading afluorescent signal generated by addition of a nucleotide in theoverhang. This step may be done by contacting the planar sample with apolymerase and a nucleotide mix, thereby adding one or more nucleotidesto the overhang; and reading a fluorescent signal generated by additionof the one or more nucleotides to the overhang.

As will be described in greater detail below, the fluorescent signal maybe generated by a variety of different methods. For example, in someembodiments, the flouorescent signal may be fluorescence from afluorescent nucleotide added to the end of the primer, or a FRET(fluorescence resonance energy transfer) signal resulting from the same.In other embodiments, the signal may generated by removing a quencherfrom a fluorescently labeled oligonucleotide that is also hybridized tothe oligonucleotide.

In any implementation of the method, the reading step may be followed byinactivating the fluorescence after reading so that other binding eventscan be detected and read. In these embodiments, the fluorescence may beinactivated by peroxide-based bleaching, cleavage of fluorophore linkedto nucleotide through cleavable linker (e.g. using TCEP as a cleavingreagent), base-exchange by exo+ polymerase such as Vent, or subsequentincorporation of quencher, for example.

Also, as will be described in greater detailed below, the method may bemultiplexed in a way that a single planar sample can be interrogated bya plurality of different capture agents, where each antibody is linkedto different oligonucleotides (i.e., oligonucleotides of differentsequence). In multiplex embodiments, the planar sample may be labeledusing at least 5, at least 10, at least 20, at least 30, at least 50, orat least 100, up to 150 or more capture agents that are each linked to adifferent oligonucleotide, and binding of the capture agents can beseparately read using a fluorescence microscope equipped with anappropriate filter for each fluorophore, or by using dual or tripleband-pass filter sets to observe multiple fluorophores. See, e.g., U.S.Pat. No. 5,776,688.

As summarized above, a capture agent used in the method may be linked toa double-stranded oligonucleotide that contains a 5′ overhang (i.e., arecessed 3′ end that can be extended by a polymerase). An example ofsuch a capture agent is shown in FIGS. 1 and 2 . In the example shown inFIG. 1B, the overhang is a single nucleotide overhang (e.g., an A),although a longer overhang (e.g., at least 2, at least 3, at least 4, atleast 5, at least 6, at least 8, at least 10, at least 20, or at leastat least 30, may be useful for other applications (e.g., multiplexedapplications). As shown in FIG. 5A-D, in certain cases, the overhang maycontain a repeated sequence, e.g., 2, 3, 4, 5, or 6 or more repeats ofthe same sequence of 2, 3, 4, 5 or 6 nucleotides, thereby allowing thecapture agent to be used in multiplexed applications as described below.In certain embodiments, the double stranded oligonucleotide may have arecessed 3′ end at the other end of the oligonucleotide (i.e., at theend closest to the capture agent). However, this end is not extendible.In certain circumstances, the double-stranded oligonucleotide maycontain one or more third oligonucleotides that are hybridized to theoverhang. In these embodiments, there will be a gap of 1, 2, 3, 4 or 5or more nucleotides between the second strand of the double-strandedoligonucleotide and the oligonucleotide that is hybridized to theoverhang (see, e.g., FIGS. 7 and 8 ). In multiplex embodiments, theplurality of capture agents may be distinguished by the sequence of theoverhang and not by the sequence of the first strand of the doublestranded oligonucleotide. In these embodiments, the second strand of thedouble stranded oligonucleotides is different for each of the captureagents.

In certain cases, the fluorophore used may be a coumarin, a cyanine, abenzofuran, a quinoline, a quinazolinone, an indole, a benzazole, aborapolyazaindacene and or a xanthene including fluorescein, rhodamineand rhodol. In multiplexing embodiments, fluorophores may be chosen sothat they are distinguishable, i.e., independently detectable, from oneanother, meaning that the labels can be independently detected andmeasured, even when the labels are mixed. In other words, the amounts oflabel present (e.g., the amount of fluorescence) for each of the labelsare separately determinable, even when the labels are co-located (e.g.,in the same tube or in the same area of the section).

Specific fluorescent dyes of interest include: xanthene dyes, e.g.,fluorescein and rhodamine dyes, such as fluorescein isothiocyanate(FITC), 6-carboxyfluorescein (commonly known by the abbreviations FAMand F), 6-carboxy-2′,4′,7′,4,7-hexachlorofluorescein (HEX),6-carboxy-4′, 5′-dichloro-2′, 7′-dimethoxyfluorescein (JOE or J),N,N,N′,N′-tetramethyl-6-carboxyrhodamine (TAMRA or T),6-carboxy-X-rhodamine (ROX or R), 5-carboxyrhodamine-6G (R6G⁵ or G⁵),6-carboxyrhodamine-6G (R6G⁶ or G⁶), and rhodamine 110; cyanine dyes,e.g., Cy3, Cy5 and Cy7 dyes; coumarins, e.g., umbelliferone; benzimidedyes, e.g. Hoechst 33258; phenanthridine dyes, e.g., Texas Red; ethidiumdyes; acridine dyes; carbazole dyes; phenoxazine dyes; porphyrin dyes;polymethine dyes, e.g., cyanine dyes such as Cy3, Cy5, etc.; BODIPY dyesand quinoline dyes. Specific fluorophores of interest that are commonlyused in subject applications include: Pyrene, Coumarin,Diethylaminocoumarin, FAM, Fluorescein Chlorotriazinyl, Fluorescein,R110, Eosin, JOE, R6G, Tetramethylrhodamine, TAMRA, Lissamine,Napthofluorescein, Texas Red, Cy3, and Cy5, etc.

Suitable distinguishable fluorescent label pairs useful in the subjectmethods include Cy-3 and Cy-5 (Amersham Inc., Piscataway, N.J.), Quasar570 and Quasar 670 (Biosearch Technology, Novato Calif.), Alexafluor555and Alexafluor647 (Molecular Probes, Eugene, Oreg.), BODIPY V-1002 andBODIPY V1005 (Molecular Probes, Eugene, Oreg.), POPO-3 and TOTO-3(Molecular Probes, Eugene, Oreg.), and POPRO3 and TOPRO3 (MolecularProbes, Eugene, Oreg.). Further suitable distinguishable detectablelabels may be found in Kricka et al. (Ann Clin Biochem. 39:114-29,2002), Ried et al. (Proc. Natl. Acad. Sci. 1992: 89: 1388-1392) andTanke et al. (Eur. J. Hum. Genet. 1999 7:2-11) and others.

In order to further illustrate the present invention, the followingspecific examples are given with the understanding that they are beingoffered to illustrate the present invention and should not be construedin any way as limiting its scope.

Example 1

In this example, the fluorescent signal may be produced by a fluorescentnucleotide that is added to the 3′ end of the primer. This method maycomprise reading a signal from the added fluorescent nucleotide, orreading a FRET signal generated by energy transfer between twofluorescent nucleotides that are added to the primer.

The example shown in FIGS. 1 and 2 shows how an antibody can be linkedto a oligonucleotide chemically, or via biotin/streptavidin interactions(FIG. 1B) and how a fluorescent signal can be generated by adding afluorescent nucleotide to the end of the primer (FIG. 2 ). In thisexample, the antigen is stained by an antibody that is coupled to a DNAdimer with an overhanging 5′ end (lower strand) and recessed 3′ end(upper strand) either chemically (FIG. 1 top panel) or throughstreptavidin (FIG. 1 bottom and middle panels).

After binding the capture agent to the tissue sample, the pattern ofbinding of the capture agent may be determined using an on-slide endfill-in reaction by using a suitable polymerase (e.g., by exo⁻ Klenow,Bst, Taq, Klentaq, or an exo⁻ Klenow—Vent mixture) and fluorescentlylabeled nucleotide (FIG. 1 and FIG. 2 top panel).

If necessary, the signal-to-noise ratio can be increased by: a)multimerization of position complementary to labeling nucleotide (FIG. 2, middle panel); or b) by generating a FRET between two nucleotides areincorporated, whereby the emission wavelength of one of the nucleotides(FIG. 2 , bottom panel C on the figure) serves as an excitationwavelength for another (FIG. 2 , bottom panel U on the figure).

Fluorescence may be inactivated before addition of subsequent stainingreagents by any convenient method including, but not limited tophotobleaching, peroxide-based bleaching, inactivation by ozone,cleavage of fluorophore linked to nucleotide through cleavable linker(e.g. using TCEP as a cleaving reagent), base-exchange by exo+polymerase such as Vent, subsequent incorporation of quencher.

In these embodiments, after fluorescence has been inactivated, themethod can be repeated, i.e., the planar sample may be re-stained usinga different antibody and fluorescence can be read.

Multiplexing

Multiplexing can be implemented using specially designedoligonucleotides using two different approaches, referred to as the“reversible terminator” and “missing base” approaches, which aredescribed in greater detail below. Both of these methods rely on acomposition comprising a plurality of (e.g., at least 5, at least 10, atleast 20, at least 30, at least 50, or at least 100, up to 150 or more)capture agents that recognize different complementary sites, wherein:each of the capture agents is linked to a double-strandedoligonucleotide that comprises a first strand and a second strand; thecapture agents are linked to a double-stranded oligonucleotide by the 5′end of first strand; the 3′ end of the first strand in each of thedouble-stranded oligonucleotides is recessed relative to the 5′ end ofthe second strand, thereby producing an overhang; and the overhang isdifferent for each of the capture agents. Examples of such compositionsare illustrated in FIGS. 3 and 4 . FIG. 3 shows a population of captureagents that have an overhang defined by the formula:3′-N_(4n)N₁/N₂/N₃-5′ followed by short stretch of random composition onthe 5′ end to increase the overall polymerase residence on the DNAduplex, where N₁, N₂, N₃ and N₄ are different nucleotides selected fromG, A, T and C and n is 0, 1 or more. FIG. 4 , on the other hand, shows apopulation of capture agents that have an overhang defined by theformula 3′-YN₁/N₂-5′, optionally followed by short stretch (e.g., 1-5residues) of random nucleotides on the 5′ end to increase the overallpolymerase residence on the DNA duplex, wherein Y is a nucleotidesequence of length n (n is 0, 1 or more) composed of bases N₃ and N₄,wherein nucleotide N₃ is in odd positions and nucleotide N₄ is in evenpositions, counting from the start of the overhang and N₁, N₂, N₃ and N₄are different nucleotides selected from G, A, T and C. As illustrated inFIGS. 3, 4 and 5 , the sequence of the first strand is the same for eachof the capture agents; and the sequence of the second strand isdifferent for each of the capture agents. In these embodiments, thedifferent second strands make the overhangs different between thedifferent capture agents.

In some embodiments, the multiplex methods generally comprise: (a)incubating a planar sample with an above-described antibody compositionunder conditions by which the capture agents bind to complementary sitesin the planar sample; (b) cross-linking the capture agents to the planarsample; (c) contacting the planar sample with a polymerase and either anincomplete nucleotide mix of labeled and unlabeled bases or a nucleotidemix where some or all bases are fluorescent and some or all basesconstitute reversible terminator nucleotides or fluorescent reversibleterminator nucleotides; and (d) reading, using fluorescence microscopy,a fluorescent signal generated by addition a nucleotide to some but notall of the capture agents. Step (c) of this method may comprise (c)contacting the planar sample with a polymerase and:

(i) a nucleotide mix that comprises fluorescent nucleotides that arecomplementary to N₁, N₂ and N₃ and a reversible terminator nucleotidethat is complementary to N₄ or (ii) a nucleotide mix that comprisesfluorescent reversible terminator nucleotides that are complementary toN₁, N₂ and N₃ and a reversible terminator nucleotide that iscomplementary to N₄ or (iii) a nucleotide mix that comprises fluorescentnucleotides that are complementary to N₁, and N₂, an unlabelednucleotide that is complementary to N₃, and no nucleotide that iscomplementary to N₄, thereby adding fluorescent nucleotides onto thedouble-stranded oligonucleotides of some but not all of the captureagents thereby adding fluorescent nucleotides onto the double-strandedoligonucleotides of some but not all of the capture agents; and (d)reading, using fluorescence microscopy, a fluorescent signal generatedby addition of a fluorescent nucleotide to some but not all of thecapture agents. Examples of such methods are described in greater detailbelow.

With reference to FIG. 6 it is expected that in the case when largerpanels of capture agents are to be employed (e.g. 100 and more) thelength of the read over the oligonucleotide overhangs may increaseaccordingly. This may or may not reduce the efficiency of staining dueto accumulation of primer extension errors along the length of theoligonucleotide duplex. To circumvent such potential source of signalloss a slight modification of design can be implemented. The pluralityof capture agents can be divided in sets such that number of captureagents in the set does exceed the capacity of the multiplexing protocolto render staining without significant signal loss (e.g. 30). Each suchset of capture agents will be conjugated to “terminated” (the last 3′base is dideoxy- or propyl-modified) upper strand oligonucleotide of thesame sequence as in the original version of the “missing base” approach.The lower strand oligos will incorporate an additional set-specificregion which will serve as a landing spot for an additional primer whichis to be on-slide hybridized to the particular subset of the totalplurality of the antibodies at the time when they are to be rendered.This approach allows not to extend the reads beyond certain thresholdand at the same time have an unlimited potential number of captureagents in the sample.

Reversible Terminator Method

This implementation of the method relies on reversible terminators,i.e., chain terminator nucleotides that can be de-protected afterincorporation, thereby allowing further nucleotides to be added to thatnucleotide.

This method can be implemented using a composition comprising aplurality of capture agents that are linked to double strandedoligonucleotides, as illustrated in FIG. 3 . In these embodiments, thetop strand of the double stranded oligonucleotide is linked to thecapture agent and is same for each antibody, and the sequence of thebottom strand varies between capture agents. As shown on FIG. 5A, the 5′end of the lower strand of the double-stranded oligonucleotide (whichforms the overhang) is of the general 3′-N_(4n)N₁/N₂/N₃-5′ followed byshort stretch of random nucleotides on the 5′ end to increase theoverall polymerase residence on the DNA duplex, where N₁, N₂, N₃ and N₄are different nucleotides selected from G, A, T and C and n is 0, 1 ormore. As shown on FIG. 5B a more general formula of loweroligonucleotide overhang 3′-XN₁/N₂/N₃-5′, where N₁, N₂, N₃ are differentnucleotides selected from G, A, T and C and X is a nucleotide stretch ofbases Xi (such that Xi are different nucleotides selected from G, A, Tand C) of random composition and length is also applicable in thismethod.

In certain embodiments, this method may comprise: (a) incubating aplanar sample with a multiplex antibody composition in which theoverhangs are of the formula 5′-N₁/N₂/N₃N₄n, wherein N₁, N₂, N₃ and N₄are different nucleotides selected from G, A, T and C and n is 1 ormore; under conditions by which the capture agents specifically bind tocomplementary sites in the planar sample; (b) cross-linking the captureagent to the planar sample; (c) contacting the planar sample with apolymerase and a nucleotide mix that comprises fluorescent nucleotidesthat are complementary to N₁, N₂ and N₃ and a reversible terminatornucleotide that is complementary to N₄; and (d) reading, usingfluorescence microscopy, a fluorescent signal generated by addition of anucleotide to some but not all of the capture agents. This cycle may berepeated by (e) inactivating the fluorescent signal, deprotecting thereversible terminator nucleotide and (f) blocking the planar sample; andrepeating steps (c) and (d). In certain embodiments, the method maycomprise repeating steps (c), (d) (e) and (f) multiple times. Thereagent used for blocking may vary depending on the chemistry used. Incertain embodiments, the sample may be blocked with a thiol-reactivecompounds such as cysteine, glutathione or iodoacetamide.

For example, this method can be implemented using a compositioncomprising: a first antibody linked to a first double strandedoligonucleotide, wherein the first double stranded oligonucleotidecomprises a single nucleotide 5′ overhang comprising base N₁; a secondantibody linked to a second double stranded oligonucleotide, wherein thesecond double stranded oligonucleotide comprises a single nucleotide 5′overhang comprising base N₂; a third antibody linked to a third doublestranded oligonucleotide, wherein the third double strandedoligonucleotide comprises a single nucleotide 5′ overhang comprisingbase N₃; a fourth antibody linked to a fourth double strandedoligonucleotide comprises a two nucleotide 5′ overhang, wherein thefirst position of the overhang comprises base N₄ and the second positionof the overhang is base N₁; a fifth antibody linked to a fifth doublestranded oligonucleotide, wherein the fifth double strandedoligonucleotide comprises a two nucleotide 5′ overhang, wherein thefirst position of the overhang comprises base N₄ and the second positionof the overhang is base N₂; and a sixth antibody linked to a sixthdouble stranded oligonucleotide, wherein the sixth double strandedoligonucleotide comprises a two nucleotide 5′ overhang, wherein thefirst position of the overhang comprises base N₄ and the second positionof the overhang is base N₃, wherein N₁, N₂, N₃ and N₄ are differentnucleotides selected from G, A, T and C. An example of such a populationof capture agents is shown in FIG. 3 .

In certain implementations, the composition may also contain a seventhantibody linked to a seventh double stranded oligonucleotide, whereinthe seventh double stranded oligonucleotide comprises a multiplenucleotide 5′ overhang, wherein the first position of the overhangcomprises base N₄, the second position of the overhang is base N₄ andthird is selected from N₁, N₂, and N₃.

In this implementation of the method, the planar sample can beco-stained simultaneously using a panel of capture agents, each labeledwith one oligonucleotide duplex designed according to the strategyoutlined on FIG. 3 . The duplexes are designed in such a way that eachantibody has the same upper strand sequence linked, covalently orthrough streptavidin, to an antibody through the 5′ end. The lowerstrand changes from antibody to antibody. In this implementation, thegeneral formula for the lower strand is 3′-dideoxydC-sequence-complimentary-to-upper-strand G_(n)A/T/C-5′. One type of lowerstrand base (nucleotide G in this example) is reserved for step-wiseprogression and its complementary pair on the upper strand is never usedin labeled form. The other three bases are complementary to labelednucleotides and can be used to identify three capture agents per cycle.In a more general case the general formula for the lower strand is3′-dideoxydC-sequence-complimentary-to-upper-strand-X-N₁/N₂/N₃-5′ whereX, of X is any nucleotide excluding one reserved for “walking base” ofthis particular cycle and X is any base as shown on FIG. 5B. This designensures that: a) no two antibody species contain the same duplex and b)only three different capture agents are detected at a time. Each cycleincludes: (a) a labeling step in which the three capture agents arelabeled and duplexes on the rest are extended one base at a time, (b) animaging step and (c) a destaining/deprotection step. During cycle tocycle transition the added fluorescent labels from the previous cycleare inactivated by any of the suitable methods, including but notlimited to: cleavage of fluorophore off the nucleotide (if the labelednucleotide is linked to the fluorophore through a cleavable linker);peroxide based bleaching; photobleaching; chemically-assistedphotobleaching; labeled base replacement by exo+ polymerase, etc. Afteror simultaneously with inactivation of the fluorophores added in theprevious reaction, the unlabeled “extension” nucleotide that has beenadded to the remainder of the capture agents is activated by cleavage ofthe protective group off its 3′ end. Cleavage of the protective group,in turn, allows that nucleotide to be extended in the next cycle. Sincethe A, T and C are reserved for incorporation of a labelled nucleotide,those nucleotides only occur at the end of each lower strand of theduplex. This approach is based on the chemical nature of reversibleterminators, which precludes upper strand extension for more than onenucleotide at a time even on polyG stretches of the lower strand.Optionally, a quencher labeled nucleotide can be incorporated followingthe labeled nucleotide. The performance of “reversible terminatormethod” as exemplified in sequential detection of CD4 and CD8 positiveT-cells in smears of mouse splenocytes is illustrated in FIG. 13A-D.

Missing Base Method

This implementation of the method relies on a “missing” base design inwhich, in each cycle, two labeled and one unlabeled nucleotides areadded to the reaction, and the “missing base” prevents the primers frombeing extended by more than a single nucleotide.

This method can be implemented using a composition comprising aplurality of capture agents that are linked to double strandedoligonucleotides, as illustrated in FIG. 4 . In these embodiments, thetop strand of the double stranded oligonucleotide is linked to thecapture agent and is same for each antibody, and the sequence of thebottom strand varies between capture agents. As shown in FIG. 4 , the 5′end of the lower strand of the double-stranded oligonucleotide (whichforms the overhang) is of the general formula 3′-YN₁/N₂-5′, optionallyfollowed by short stretch (e.g., 1-5 residues) of random nucleotides onthe 5′ end to increase the overall polymerase residence on the DNAduplex, wherein Y is a nucleotide sequence of length n (n is 0, 1 ormore) composed of bases N₃ and N₄, wherein nucleotide N₃ is in oddpositions and nucleotide N₄ is in even positions, counting from thestart of the overhang and N₁, N₂, N₃ and N₄ are different nucleotidesselected from G, A, T and C.

Also a more general formula 3′-YN₁/N₂-5′, wherein N₁, N₂, N₃ and N₄ aredifferent nucleotides selected from G, A, T and C and Y is a nucleotidesequence of length n (n is 0, 1 or more) composed of alternating randomlength stretches of bases N₃ and N₄ such that the order number ofN₃—stretches is odd and of N₄ stretches is even, may be applicable inthis method

In certain embodiments, this method may comprise: (a) incubating aplanar sample with a multiplex antibody composition in which theoverhangs are of the formula (3′-YN₁/N₂-5′) described in the priorparagraph; under conditions by which the capture agents specificallybind complementary sites in the planar sample; (b) cross-linking thecapture agent to the planar sample; (c) contacting the planar samplewith a polymerase and a nucleotide mix that comprises fluorescentnucleotides that are complementary to N₁, and N₂, an unlabelednucleotide that is complementary to N₃ and no nucleotide that iscomplementary to N₄; and (d) reading, using fluorescence microscopy, afluorescent signal generated by addition of a nucleotide to some but notall of the capture agents. This cycle may be repeated by (e)inactivating the fluorescent signal, (f) blocking the sample andcontacting the planar sample with a polymerase and an unlabelednucleotide that is complementary to N₄; and repeating steps (c) (d). Incertain embodiments, the method may comprise repeating steps (c), (d),(e) and (f) multiple times.

This method can be implemented using a capture agent composition thatcomprises: a first antibody linked to a first double strandedoligonucleotide, wherein the first double stranded oligonucleotidecomprises a single nucleotide 5′ overhang comprising base N₁; a secondantibody linked to a second double stranded oligonucleotide, wherein thesecond double stranded oligonucleotide comprises a single nucleotide 5′overhang comprising base N₂; a third antibody linked to a fourth doublestranded oligonucleotide, wherein the third double strandedoligonucleotide comprises a two nucleotide 5′ overhang, wherein thefirst from the 3′ position of the overhang comprises base N₄ and thesecond position comprises N₁; and a fourth antibody linked to a fourthdouble stranded oligonucleotide, wherein the fourth double strandedoligonucleotide comprises a two nucleotide 5′ overhang, wherein thefirst position of the overhang comprises base N₄ and the second positioncomprises base N₂, wherein N₁, N₂, N₃ and N₄ are different nucleotidesselected from G, A, T and C. An example of such a population of captureagents is shown in FIG. 4 .

In certain implementations, the composition may also contain a fifthantibody linked to a fifth double stranded oligonucleotide, wherein thefifth double stranded oligonucleotide comprises a multiple nucleotide 5′overhang, wherein the first position of the overhang comprises base N₄,the second position comprises base N₃, and the third position comprisesN₁ or N₂.

Overall there is no theoretical limits to the number of co-detectedcomplementary sites, e.g., antigens, both in the case of “reversibleterminator” and of “missing base” approach

The missing base approach does not use reversible terminators. Instead,extension of a single nucleotide is ensured by using two interchangingbases (e.g., T and C as shown in FIG. 4 instead of the corresponding Gin the “reversible terminators” approach) and adding only one of the twodNTPs at a time in the primer extension reaction. After theincorporation of the first nucleotide, the absence of the second dNTPcauses strand elongation to stall, thereby ensuring that the primers areextended by only a single nucleotide. As in the previous strategy, allcomplementary sites can be co-stained simultaneously using captureagents, each labeled with a specific oligonucleotide duplex.

In this embodiment, the duplexes can be designed using the strategyshown in FIG. 4 , i.e., in such a way that each antibody has the sameupper stand oligonucleotide sequence linked to it via covalent bond orthrough a streptavidin-biotin interaction. In this implementation, thelower strand changes from antibody to antibody. In this method, thegeneral formula for the lower strand is 3′ ddC-sequence-complimentary-to-upper-strand —YA/N₂-5′ where Y is composed ofbases T and C such that T can be found only in even and C only at oddpositions. Or in the more general case 3′-YN₁/N₂-5′, wherein N₁, N₂, N₃and N₄ are different nucleotides selected from G, A, T and C and Y is anucleotide sequence of length n (n is 0, 1 or more) composed ofalternating random length stretches of bases N₃ and N₄ such that theorder number of N₃—stretches is odd and of N₄ stretches is even. In thefirst simple implementation two base pairs of the lower strand (T and Cas in exemplary design on FIG. 4 ) are reserved for step-wiseprogression and their complementary pair on the upper strand is neverlabeled. The other two bases are complementary to labeled nucleotidesand can render the staining with two different capture agents per cycle.Such design ensures that a) no two capture agents contain the sameduplex and b) only two different antibody are read per cycle. In thisimplementation, each cycle can have three steps: a labeling step inwhich the two capture agents are labeled by incorporation of fluorescentdNTPs and all of the other duplexes are extended one base at a time, animaging step, and a de-staining/reactivation step.

During cycle-to-cycle transition the labeled capture agents from theprior cycle can be bleached/destained in the same way as describedabove. Optionally, instead of bleaching, a quencher labeled nucleotidecan be incorporated after the labeled base. Because, in this embodiment,the position that is labeled is the last position in the overhang, thelabeled capture agents from prior cycle cannot be re-labeled in latercycles because all nucleotide positions in the overhang have been filledin. The performance of “reversible terminator method” as exemplified insequential detection of CD4 and CD8 positive T-cells in smears of mousesplenocytes is illustrated in FIG. 13, 15 and FIG. 16 .

Exemplary Method 2

In this method, extension of a primer by nick translation removes aquencher from a fluorescently labeled “detector” oligonucleotide that ishybridized to the lower strand oligonucleotide in such a way that ispositioned downstream from the upper strand primer. The principles ofthis method are illustrated in FIG. 7 . A multiplexed version of thismethod is shown in FIG. 8 .

In certain embodiments, the multiplexed implementations may comprise:(a) incubating the planar sample with a plurality of capture agents thatare linked to a double-stranded oligonucleotide; (b) crosslinking thecapture agents to the planar sample; (c) extending a primer that ishybridized to the oligonucleotide of a first set of capture agents ofthe plurality, thereby generating a first set of fluorescent signals(e.g., by removing the quencher from a labeled oligonucleotide that ishybridized to the oligonucleotide downstream from the primer); (d)reading the first set of fluorescent signals using fluorescencemicroscopy; (e) inactivating the fluorescence; (f) extending a primerthat is hybridized to the oligonucleotide of a second set of captureagents of the plurality, thereby generating a second set of fluorescentsignals (e.g., by removing the quencher from a labeled oligonucleotidethat is hybridized to the oligonucleotide downstream from the primer);(g) reading the second set of fluorescent signals using fluorescencemicroscopy; and (h) comparing the images produce in steps (d) and (g).

In this method, the architecture of the double-stranded oligonucleotideslinked to the capture agent has a specific design which is effectivelyenabling rendering of the capture agent binding pattern by “nicktranslation”. In particular the duplex of the upper strand and the lowerstrand oligo with long 5′ overhang of the lower strand is furtherhybridized to a small detector oligonucleotide labeled both byfluorescent and the quencher. There is a predesigned gap between theinitial upper strand and the upper strand detector oligo. During cyclicstaining this gap is “walked” by either “reversible terminator” or“missing base” (similar to described in previous sections) until the gapis reduced to a single base nick. Extension and progression through thenick on the upper strand by “nick translating” polymerase such as DNApol I removes the quencher from some but not all of the quenchedfluorescently labeled oligonucleotides, thereby generating a fluorescentsignal for some but not all of the capture agents.

In some embodiments the method generally comprises: (i) labeling aplanar sample with: i. a first antibody, wherein the first antibody islinked to a first oligonucleotide duplex comprising, lower strandoligonucleotide with a unique sequence hybridized thereto: (i) anoligonucleotide upper strand “primer” and (ii) a labeled upper strandoligonucleotide comprising a 5′ quencher at a site that is downstreamfrom the primer; and a fluorophore downstream from the quencher and ii.a second antibody, wherein the second antibody is linked to a secondoligonucleotide duplex comprising, lower strand oligonucleotide withunique sequence hybridized thereto: (i) an oligonucleotide upper strand“primer” and (ii) an upper strand oligonucleotide labeled both byfluorophore and a quencher; wherein the gap between the 3′ end of theprimer and the 5′ end of the labeled oligonucleotide is different forthe first and second oligonucleotides; (ii) incubating the tissue samplewith a first nucleotide mix and a polymerase, thereby removing thequencher from only the labeled oligonucleotide that is hybridized to thefirst oligonucleotide and producing a first fluorescent signal; (iii)reading the first fluorescent signal using fluorescence microscopy; (iv)inactivating the fluorescent signal by further progression ofnick-translating polymerase; (v) incubating the tissue sample with asecond nucleotide mix and a polymerase, thereby removing the quencherfrom only the labeled oligonucleotide that is hybridized to the secondoligonucleotide and producing a first fluorescent signal; and (vi)reading the second fluorescent signal from the planar sample usingfluorescence microscopy.

FIGS. 7 and 8 show an example of this method. The multiplexing methodshown in FIG. 8 has the following steps:

Step 1: The planar sample is stained by capture agents that are coupledto a DNA double-stranded oligonucleotide chemically or throughstreptavidin (as described in FIG. 1 ) such that the top strand of theduplex contains a nick or a single base deletion followed by anucleotide stretch bordered by a fluorophore and its quencher on twoends (“molecular beacon” or Taqman based design).

Step 2: Staining pattern is rendered by a nick-translation reactioncarried out by any 5′ exo+ polymerase such as DnaPoII Klenow fragment inthe presence of a single letter (A as in FIG. 5 for example). Nicktranslation removes the quencher but stops before removing the part ofthe duplex with the fluorophore.

Step 3: For rendering of other staining reagents, the fluorescence isremoved by continuing nick translation in the presence of the letters ofthe stretch bearing the fluorophore.

Step 4: When multiplexing is desired, multiplexing can be achieved byspecial design of oligo duplexes attached to detection reagents. Inparticular each antibody set (two or three per cycle) has a gap of anincreasing length between the top strand priming and the detectoroligonucleotide. This sequence gap on the strand bearing thequencher/fluorophore pair is filled up to final nick in such a way thatsingle base is extended per cycle, similar to how it is achieved inmethod 1 (see FIG. 8 ).

Exemplary Method 3

In this implementation, the method comprises rending antibody stainingby primer extension with a fluorophore labeled base or otherwise readinga FRET signal generated by energy transfer between a first fluorescentnucleotide added to the primer by primer extension and a secondnucleotide that is present in the oligonucleotide FIG. 10 .

The principles of this method are illustrated in FIG. 9A. Themultiplexing is achieved by removing the extension priming oligo bymelting the duplex or by exonuclease and reannealing another primeroligo which is extendable on a different antibody. A multiplexed versionof this method is shown in FIG. 9B. In certain embodiments, themultiplexed implementations may comprise: (a) incubating the planarsample with a plurality of capture agents; (b) cross-linking the captureagents to the planar sample; (c) extending a primer that is hybridizedto the oligonucleotide of a first set of capture agents of the plurality(e.g., wherein the 3′ end of the first primer anneals to only theoligonucleotide of the first population), thereby generating a first setof fluorescent signals; (d) reading the first set of fluorescent signalsusing fluorescence microscopy; (e) inactivating the fluorescence; (f)extending a primer that is hybridized to the oligonucleotide of a secondset of capture agents of the plurality (e.g., wherein the 3′ end of thefirst primer anneals to only the oligonucleotide of the secondpopulation), thereby generating a second set of fluorescent signals; (g)reading the second set of fluorescent signals using fluorescencemicroscopy; and (h) comparing the images produce in steps (d) and (g).

In certain embodiments, this method comprises: (a) incubating the planarsample with (i) a first antibody that is linked to a first labeledoligonucleotide and (ii) a second antibody that is linked to a secondlabeled oligonucleotide, (b) cross-linking the capture agents to theplanar sample; (c) hybridizing the first and second labeledoligonucleotides with a first primer, wherein the 3′ end of the firstprimer anneals to only the first labeled oligonucleotide; (d) extendingthe primer with a fluorescent nucleotide; (e) reading, by fluorescencemicroscopy, a FRET signal generated by energy transfer between the labelof the first oligonucleotide and the fluorescent nucleotide added to thefirst primer; (f) inactivating the fluorescent nucleotide added to thefirst primer; (g) hybridizing the first and second labeledoligonucleotides with a second primer, wherein the 3′ end of the secondprimer anneals to only the second labeled oligonucleotide; (h) extendingthe second primer with a fluorescent nucleotide; and (i) reading, byfluorescence microscopy, a FRET signal generated by energy transferbetween the label of the second oligonucleotide and the fluorescentnucleotide added to the second primer.

FIGS. 9-10 shows an example of this method. The method shown in FIGS.8-11 has the following steps:

Step 1: The planar sample is stained using a capture agent that iscoupled to a single stranded oligonucleotide. The oligonucleotide couldbe either unlabeled or labeled by FRET acceptor (e.g. Cy5) fluorophoreon the 3′ end.

Step 2: The binding pattern can be determined by an on-slidehybridization of a complementary probe followed a primer extensionreaction in which a fluorescently labeled nucleotide fills in theoverhang in the extended strand. In this example (see FIG. 10 ) theextended base is labeled by a FRET donor (e.g. Cy3), which can increasethe signal to noise ratio. If the oligonucleotide that is linked to thecapture agent is unlabeled, then the fluorescent emission of thenucleotide that has been incorporated by DNA synthesis can be detecteddirectly, without FRET FIG. 9 .

Step 3: The binding pattern of other capture agents can be determined byremoving the fluorescence by cleavage of lower strand by exo+ DNApolymerase such as Vent (FIG. 9 ). Alternatively, the fluorescence canbe removed by raising the temperature beyond the melting point of theDNA strands or by one of the de-staining techniques describedpreviously.

Step 4: Multiplexing can be achieved by staining of the sample with alibrary of capture agents each labeled with specific oligonucleotidesand cycling through Steps 1-3, as described above, each time using adifferent detection oligonucleotide that is complementary to one of thecapture agent-conjugated oligonucleotides. Only duplexes where primersare annealed specifically will be properly extended (FIG. 11 ). In theseembodiments, each primers is designed so that its 3′ end hybridizes toonly one of the oligonucleotides that are linked to a capture agent.

Utility

The planar sample may be a section of a tissue biopsy obtained from apatient. Biopsies of interest include both tumor and non-neoplasticbiopsies of skin (melanomas, carcinomas, etc.), soft tissue, bone,breast, colon, liver, kidney, adrenal, gastrointestinal, pancreatic,gall bladder, salivary gland, cervical, ovary, uterus, testis, prostate,lung, thymus, thyroid, parathyroid, pituitary (adenomas, etc.), brain,spinal cord, ocular, nerve, and skeletal muscle, etc.

In certain embodiments, capture agents specifically bind to biomarkers,including cancer biomarkers, that may be proteinaceous or a nucleicacid. Exemplary cancer biomarkers, include, but are not limited tocarcinoembryonic antigen (for identification of adenocarcinomas),cytokeratins (for identification of carcinomas but may also be expressedin some sarcomas), CD15 and CD30 (for Hodgkin's disease), alphafetoprotein (for yolk sac tumors and hepatocellular carcinoma), CD117(for gastrointestinal stromal tumors), CD10 (for renal cell carcinomaand acute lymphoblastic leukemia), prostate specific antigen (forprostate cancer), estrogens and progesterone (for tumouridentification), CD20 (for identification of B-cell lymphomas) and CD3(for identification of T-cell lymphomas).

The above-described method can be used to analyze cells from a subjectto determine, for example, whether the cell is normal or not or todetermine whether the cells are responding to a treatment. In oneembodiment, the method may be employed to determine the degree ofdysplasia in cancer cells. In these embodiments, the cells may be asample from a multicellular organism. A biological sample may beisolated from an individual, e.g., from a soft tissue. In particularcases, the method may be used to distinguish different types of cancercells in FFPE samples.

The method described above finds particular utility in examining planarsamples using a plurality of antibodies, each antibodies recognizing adifferent marker. Examples of cancers, and biomarkers that can be usedto identify those cancers, are shown below. In these embodiments, onedoes not need to examine all of the markers listed below in order tomake a diagnosis.

Acute Leukemia IHC Panel CD3, CD7, CD20, CD34, CD45, CD56, CD117, MPO,PAX-5, and TdT. Adenocarcinoma vs. Mesothelioma IHC Pan-CK, CEA, MOC-31,BerEP4, TTF1, calretinin, and WT-1. Panel Bladder vs. Prostate CarcinomaIHC Panel CK7, CK20, PSA, CK 903, and p63. Breast IHC Panel ER, PR,Ki-67, and HER2. Reflex to HER2 FISH after HER2 IHC is available.Burkitt vs. DLBC Lymphoma IHC panel BCL-2, c-MYC, Ki-67. CarcinomaUnknown Primary Site, Female CK7, CK20, mammaglobin, ER, TTF1, CEA,CA19-9, S100, (CUPS IHC Panel - Female) synaptophysin, and WT-1.Carcinoma Unknown Primary Site, Male CK7, CK20, TTF1, PSA, CEA, CA19-9,S100, and (CUPS IHC Panel - Male) synaptophysin. GIST IHC Panel CD117,DOG-1, CD34, and desmin. Hepatoma/Cholangio vs. Metastatic HSA (HepPar1), CDX2, CK7, CK20, CAM 5.2, TTF-1, and Carcinoma IHC Panel CEA(polyclonal). Hodgkin vs. NHL IHC Panel BOB-1, BCL-6, CD3, CD10, CD15,CD20, CD30, CD45 LCA, CD79a, MUM1, OCT-2, PAX-5, and EBER ISH. LungCancer IHC Panel chromogranin A, synaptophysin, CK7, p63, and TTF-1.Lung vs. Metastatic Breast Carcinoma IHC TTF1, mammaglobin, GCDFP-15(BRST-2), and ER. Panel Lymphoma Phenotype IHC Panel BCL-2, BCL-6, CD3,CD4, CD5, CD7, CD8, CD10, CD15, CD20, CD30, CD79a, CD138, cyclin D1,Ki67, MUM1, PAX-5, TdT, and EBER ISH. Lymphoma vs. Carcinoma IHC PanelCD30, CD45, CD68, CD117, pan-keratin, MPO, S100, and synaptophysin.Lymphoma vs. Reactive Hyperplasia IHC BCL-2, BCL-6, CD3, CD5, CD10,CD20, CD23, CD43, cyclin Panel D1, and Ki-67. Melanoma vs. Squamous CellCarcinoma CD68, Factor XIIIa, CEA (polyclonal), S-100, melanoma IHCPanel cocktail (HMB-45, MART-1/Melan-A, tyrosinase) and Pan-CK. MismatchRepair Proteins IHC Panel MLH1, MSH2, MSH6, and PMS2. (MMR/Colon Cancer)Neuroendocrine Neoplasm IHC Panel CD56, synaptophysin, chromogranin A,TTF-1, Pan-CK, and CEA (polyclonal). Plasma Cell Neoplasm IHC PanelCD19, CD20, CD38, CD43, CD56, CD79a, CD138, cyclin D1, EMA, kappa,lambda, and MUM1. Prostate vs. Colon Carcinoma IHC Panel CDX2, CK 20,CEA (monoclonal), CA19-9, PLAP, CK 7, and PSA. Soft Tissue Tumor IHCPanel Pan-CK, SMA, desmin, S100, CD34, vimentin, and CD68. T-CellLymphoma IHC panel ALK1, CD2, CD3, CD4, CD5, CD7, CD8, CD10, CD20, CD21,CD30, CD56, TdT, and EBER ISH. T-LGL Leukemia IHC panel CD3, CD8,granzyme B, and TIA-1. Undifferentiated Tumor IHC Panel Pan-CK, S100,CD45, and vimentin.

In some embodiments, the method may involve obtaining an image asdescribed above (an electronic form of which may have been forwardedfrom a remote location) and may be analyzed by a doctor or other medicalprofessional to determine whether a patient has abnormal cells (e.g.,cancerous cells) or which type of abnormal cells are present. The imagemay be used as a diagnostic to determine whether the subject has adisease or condition, e.g., a cancer. In certain embodiments, the methodmay be used to determine the stage of a cancer, to identify metastasizedcells, or to monitor a patient's response to a treatment, for example.

In any embodiment, data can be forwarded to a “remote location”, where“remote location,” means a location other than the location at which theimage is examined. For example, a remote location could be anotherlocation (e.g., office, lab, etc.) in the same city, another location ina different city, another location in a different state, anotherlocation in a different country, etc. As such, when one item isindicated as being “remote” from another, what is meant is that the twoitems can be in the same room but separated, or at least in differentrooms or different buildings, and can be at least one mile, ten miles,or at least one hundred miles apart. “Communicating” informationreferences transmitting the data representing that information aselectrical signals over a suitable communication channel (e.g., aprivate or public network). “Forwarding” an item refers to any means ofgetting that item from one location to the next, whether by physicallytransporting that item or otherwise (where that is possible) andincludes, at least in the case of data, physically transporting a mediumcarrying the data or communicating the data. Examples of communicatingmedia include radio or infra-red transmission channels as well as anetwork connection to another computer or networked device, and theinternet or including email transmissions and information recorded onwebsites and the like. In certain embodiments, the image may be analyzedby an MD or other qualified medical professional, and a report based onthe results of the analysis of the image may be forwarded to the patientfrom which the sample was obtained.

In some cases, the method may be employed in a variety of diagnostic,drug discovery, and research applications that include, but are notlimited to, diagnosis or monitoring of a disease or condition (where theimage identifies a marker for the disease or condition), discovery ofdrug targets (where the a marker in the image may be targeted for drugtherapy), drug screening (where the effects of a drug are monitored by amarker shown in the image), determining drug susceptibility (where drugsusceptibility is associated with a marker) and basic research (where isit desirable to measure the differences between cells in a sample).

In certain embodiments, two different samples may be compared using theabove methods. The different samples may be composed of an“experimental” sample, i.e., a sample of interest, and a “control”sample to which the experimental sample may be compared. In manyembodiments, the different samples are pairs of cell types or fractionsthereof, one cell type being a cell type of interest, e.g., an abnormalcell, and the other a control, e.g., normal, cell. If two fractions ofcells are compared, the fractions are usually the same fraction fromeach of the two cells. In certain embodiments, however, two fractions ofthe same cell may be compared. Exemplary cell type pairs include, forexample, cells isolated from a tissue biopsy (e.g., from a tissue havinga disease such as colon, breast, prostate, lung, skin cancer, orinfected with a pathogen etc.) and normal cells from the same tissue,usually from the same patient; cells grown in tissue culture that areimmortal (e.g., cells with a proliferative mutation or an immortalizingtransgene), infected with a pathogen, or treated (e.g., withenvironmental or chemical agents such as peptides, hormones, alteredtemperature, growth condition, physical stress, cellular transformation,etc.), and a normal cell (e.g., a cell that is otherwise identical tothe experimental cell except that it is not immortal, infected, ortreated, etc.); a cell isolated from a mammal with a cancer, a disease,a geriatric mammal, or a mammal exposed to a condition, and a cell froma mammal of the same species, preferably from the same family, that ishealthy or young; and differentiated cells and non-differentiated cellsfrom the same mammal (e.g., one cell being the progenitor of the otherin a mammal, for example). In one embodiment, cells of different types,e.g., neuronal and non-neuronal cells, or cells of different status(e.g., before and after a stimulus on the cells) may be employed. Inanother embodiment of the invention, the experimental material is cellssusceptible to infection by a pathogen such as a virus, e.g., humanimmunodeficiency virus (HIV), etc., and the control material is cellsresistant to infection by the pathogen. In another embodiment, thesample pair is represented by undifferentiated cells, e.g., stem cells,and differentiated cells.

The images produced by the method may be viewed side-by-side or, in someembodiments, the images may be superimposed or combined. In some cases,the images may be in color, where the colors used in the images maycorrespond to the labels used.

Cells any organism, e.g., from bacteria, yeast, plants and animals, suchas fish, birds, reptiles, amphibians and mammals may be used in thesubject methods. In certain embodiments, mammalian cells, i.e., cellsfrom mice, rabbits, primates, or humans, or cultured derivativesthereof, may be used.

EXPERIMENTAL Preliminary Data

To explore the possibility of in situ staining by primer extensionexpression of CD4 was visualized in mouse spleen cells in suspension(FIG. 11 ) or immobilized on a slide. (FIG. 12 ). To visualize the Tlymphocytes spleen cells were co-stained with conventional TcrB-Ax488antibody. Both samples were stained with CD4 antibody conjugated tooligo duplex as in (FIG. 11A). No Klenow polymerase was added in controlsamples which results in no separation of TcrB positive T-cells intosubsets (FIG. 11 B). When Klenow polymerase was supplied. CD4 positiveT-cells could be observed as a Cy5 positive subset of TcrB positiveT-cells (FIG. 11 C and FIG. 12 ). Clear membrane staining pattern wasobserved by confocal imaging of cells stained on-slide (FIG. 12A). Takentogether this data shows that on-slide primer extension reaction can beused for rendering the capture agent binding pattern

FIG. 11 . Flow cytometric analysis of mouse spleen cells stained byprimer extension. Mouse spleen cells were fixed and permeabilized withmethanol as done for intracellular protein staining. Cells wereco-stained with conventional TcrB-Ax488 antibody and CD4 antibodyconjugated to oligo duplex as in (A). After staining cells were eitherincubated in extension buffer with dUTP-Cy5 without (B) or with (C)Klenow exo⁻ polymerase. Note that TcrB positive T-cells in (B) areindicated by Ax-488 staining. Dependent upon the addition of Klenow,TcrB positive CD4 positive T-cells are seen as a Cy5 positive subset ofTcrB positive T-cells in (C).

FIG. 12 . On-slide analysis of mouse spleen cells stained by primerextension. Mouse spleen cells were fixed and permeabilized with methanolas done for intracellular protein staining. Cells were attached topoly-Lysine coated slide and co-stained with conventional TcrB-Ax488antibody and CD4 antibody conjugated to oligo duplex as in FIG. 12 A.After staining, cells were incubated in extension buffer with dUTP-Cy5Klenow exo⁻ polymerase and visualized by confocal microscopy. Shown areDIC image in C, Cy5 channel in A, Ax488 channel in B and merged Ax488and Cy5 channels in D. Note that only a subset of TcrB-Ax488 positiveT-cells in (B) are rendered Cy5 positive CD4 positive T-cells by primerextension as seen in (A). The membrane pattern of CD4 points tospecificity of staining by primer extension as it takes place at aparticular expected subcellular localization.

To prove the possibility of multiplexed detection of several antigens byprimer extension, the expression of CD4 and CD8 was co-analyzed in mousespleen cells immobilized on a slide by Method 1 and, specifically, themultiplexing approach based on “reversible terminators”. The cells weresimultaneously stained by CD4 and CD8 antibodies conjugated to oligoduplexes as in (FIG. 14A) simultaneously. Two cycles of rendering wereperformed such that CD8 was visualized in the first cycle (FIG. 14 C)and CD4 in the second (FIG. 14 D). Cells were counterstained withTcrB-Ax488 to delineate T-lymphocytes in the spleen cells. As expectedCD4 positive cells were rendered as a subset of TcrB positive T-cellsmutually exclusive with CD8-positive subset of T-lymphocytes (FIG.14A-D). Our data suggests that rendering antibody staining by polymer(DNA-duplex) extension is an approach enabling sensitive antigendetection and multiplexing.

FIG. 13 . Two cycle analysis of CD4 and CD8 staining in mouse spleenusing Method 1 with reversible terminators. Mouse spleen cells werefixed and permeabilized with methanol as done for intracellular proteinstaining. Cells were attached to poly-Lysine coated slide and co-stainedwith conventional TcrB-Ax488 antibody and a mixture of CD4 and CD8antibodies conjugated to oligos as indicated on (A). For the first cycleof staining the cells were incubated in extension buffer with Illuminareversible terminators and Klenow exo⁻ polymerase and visualized byconfocal microscopy (C). Following the imaging after the first cycle,cells were destained by Illumina cleavage buffer containing TCEP.Following destaining-terminator reactivation, cells were again incubatedin extension buffer with Illumina reversible terminators and Klenow exo⁻polymerase and visualized by confocal microscopy (D) Note that fourT-cells identified by high levels of TcrB and marked by four whitearrows on (B). It becomes evident after the first cycle of staining thattwo of these cells are CD8a positive (marked by purple arrows on (C).Second cycle of staining reveals that the other two cells are CD4positive (marked by green arrows on (D). The expected mutual exclusivityof CD4 and CD8a as well as membrane pattern of incorporated labelednucleotide further supports the specificity of staining by cycles ofprimer extension.

The “missing base” multiplexing approach was tested on a model ofheterogeneous tissue containing multiplicity of distinct cellularsubsets (FIG. 14 ). To this end leukocytes from homogenized mouse spleenwere divided into 30 samples. 30 different versions of CD45 were made byconjugating purified CD45 to common upper strand oligo and thenseparately annealing 30 different lower strand oligonucleotides designedto create overhangs that can be sequentially rendered (two per cycle) inthe multiplexed version of “missing base approach”. The samples wereindividually stained (barcoded) by 30 CD45 antibody conjugates, theunbound CD45 was washed off the barcoded samples were mixed and attachedto a slide. The staining of this mixture of pseudotyped cells wasrendered by “missing base” approach. Six first cycles (12 populations, 2red and green per cycle) as well as inactivation of fluorescence bycleaving the fluorophore off the modified base by TCEP between thecycles is shown on FIG. 15 . As can be seen no same two cells arestained in each cycle and between the cycles proving that on-cell primerextension reliably renders the specific antibody staining.

Materials and Methods

Spleen cells fixed in 2% formaldehyde, permeablized and stored inmethanol at−80 were spun from methanol, resuspended and washed withbuffer 4 (10 mM Tris &.5, 10 mM MgCl2, 150 mM NaCl, 0.1% Triton ×100)for 5 min on a rotator. To block against non-specific binding ofab-oligo complexes cells were further spun, resuspended in 1 ml PBS,0.5% BSA (SM) and supplemented up to additional 0.5M NaCl (0.9 ml SM+100ul 5M NaCl). 20 ul of sheared ssDNA (10 mg/ml), 50 ul of mouse IgG (10mg/ml) and 20 ul of 0.5M EDTA were further added to 1 ml of cells andthe mix was incubated for 30 min on a rotator. For staining cells wereredistributed into 30 250 ul tubes (PCR strip tubes is a convenientchoice for that matter) with premade antibody/oligo complexes (0.2 ug ofCD45-146 complex was annealed with 1 ul of specific oligo (147 etc) pertube 30 min at 40 C) and incubated for 1 h with rotation. Cells werewashed in (PBS, 0.1% Triton 0.5M salt 5 mM EDTA) twice, placed onpoly-lysine treated glass coverslips, allowed to stand/attach for 10 minand further fixed with 5 mM BS3 (7.4 mg per 4 ml) in PBS, 0.1% Triton,0.5M NaCl, 5 mM EDTA for 1 hour.

Staining was rendered in cycles. For odd cycles (1,3,5,7,9,11,13,15)coverslips were incubated for 2 min in dG/dU mix (150 nM dG, 150 nMdUssCy5, 150 nM dCssCy3, 25 ul NEB exo− Klenow per ml in buffer #4 (10mM Tris 7.5, 0.5M NaCl, 0.1% Triton ×100, 10 mM MgCl2)), washed twicewith 405 (buffet #4 supplemented up to 0.65M NaCl); and imaged byconfocal microscopy. Following imaging the fluorophores were cleaved offcells by incubation in 50 mM TCEP for 2 min in buffer 405E (10 mM Tris7.5, 0.5M NaCl, 0.1% Triton ×100, 5 mM EDTA). After cleavage cells werewashed in 405E and blocked for for 1 min in iodoacetamide solution(FRESHLY made 100 mM iodoacetamide in buffer 405E). The blockingsolution was removed by two washes with buffer #4. Before proceeding tonext cycle cells were again imaged by confocal microscopy. Even cycles(2,4,6,8,10,12, 14) were performed same as odd cycles except forsubstitution of dG with dA in labeling step and extension of cleavage to4 min at room temperature.

Results

In order to test the performance and multiplexing capacity of “missingbase” method the following model approach was employed FIGS. 14 and 15 .Mouse CD45 antibody was chemically conjugated to an “upper strand” oligo(oligo id-146). The conjugated antibody was further divided andseparately annealed (by 30 min co-incubation at 40C) to 30 different“lower strand” oligonucleotides—thus effectively creating 30 differentspecies of CD45 antibody. The 30 “lower strand” oligonucleotides weredesigned in accordance with “missing base” strategy and in addition insuch a way that 2 antibodies could be rendered per cycle using two bases(dUTP and dCTP) reversibly (through s-s linker) coupled with distinctfluorophores (Cy5 and Cy3). 30 samples of homogenized mouse spleen havebeen “barcoded” with these CD45-oligo duplex complexes such way thatmajority of cells in each sample became labeled with a particularCD45-upper/lower oligo combination. Following staining and washing thesamples were combined to mimic a tissue with 30 different cellularsubsets. The mixture was smeared on a slide and rendered by cyclingstaining with a “missing base” approach such that two subsets perstaining cycle were co-visualized on different imaging channels.

1-21. (canceled)
 22. A composition comprising: (a) a plurality ofcapture agents, wherein the plurality of capture agents can specificallybind to different complementary sites in biological sample, wherein eachof the plurality of capture agents comprises a double stranded nucleicacid, and wherein a 3′ end of a first strand of the double strandednucleic acid is recessed relative to a 5′ end of the second strand ofthe double stranded nucleic acid, thereby producing a 5′ overhang; (b) apolymerase; (c) a plurality of nucleotides; wherein the polymerase isconfigured to extend a strand of the double stranded nucleic acid withthe plurality of nucleotides.
 23. The composition of claim 22, whereinthe plurality of nucleotides comprise a fluorescent nucleotide.
 24. Thecomposition of claim 22, wherein all nucleotide of the plurality ofnucleotides are fluorescent.
 25. The composition of claim 22, whereinthe plurality of nucleotides is an incomplete nucleotide mix.
 26. Thecomposition of claim 22, wherein the plurality of nucleotides comprisereversible terminator nucleotides or fluorescent reversible terminatornucleotides.
 27. The composition of claim 22, further comprising afluorescently labeled oligonucleotide complementary to a sequence of anoverhang of at least one capture agent of the plurality of captureagents.
 28. The composition of claim 27, wherein the fluorescentlylabeled oligonucleotide comprises a quencher.
 29. The composition ofclaim 28, wherein the quencher is configured to be removed uponextension of a strand of the double stranded nucleic acid with theplurality of nucleotides.
 30. The composition of claim 22, wherein anoverhang of a double stranded nucleic acid of a first capture agent ofthe plurality of capture agents comprises a different sequence than anoverhang of a second capture agent.
 31. The composition of the claim 22,wherein the plurality of capture agents comprise an antibody, aptamer,or oligonucleotide probe.
 32. The composition of claim 22, wherein thedifferent complementary sites comprise protein epitopes or complementarynucleic acids.
 33. The composition of claim 22, wherein a sequence ofthe first strand is the same for each capture agent of the plurality ofcapture agents.
 34. The composition of claim 1, wherein the plurality ofnucleotides is an incomplete nucleotide mix.
 35. The composition ofclaim 22, wherein the plurality of capture agents comprise at least 5capture agents.
 36. The composition of claim 22, wherein the pluralityof capture agents comprise at least 10 capture agents.